The present invention relates to epsilon-polylysine silicon nanoparticles and a preparation method thereof. According to the epsilon-polylysine silicon nanoparticles, a cation type epsilon-polylysine core shell is modified on the surface layer of the nano-silicon inner core. The preparation method is that: tetraethoxysilane is hydrolyzed in a water-in-oil microemulsion system to directly prepare silica nanoparticles; the silica nanoparticles are combined with the epsilon-polylysine to obtain the epsilon-polylysine silicon nanoparticles. The epsilon-polylysine silicon nanoparticles prepared by the preparation method of the present invention have advantages of simple preparation method, good biocompatibility, no cell toxicity, and absorption of DNA and other materials with negative charge, and can be used as a novel gene vector or a chromatographic packing.